To implement:
info.pl FILE
I stored a lot of the information in a matrix. if you want to see the matrix, unsupress print in line 191-198 The matrix printed out will be in the form: SEQUENCE1 SEQUENCE2 SEQUENCE3 Number of A Number of U Number of C Number of G Number of Gap Probability of A Probability of U " " of C " " of G " " of Gap Entropy
To see the matrix, unsupress line 191-198 To see the joint distribution: Unsupress line 149-1521 To see mutual information, unsupress 170-173
AnalysisOfData
Extra Credit
This 3D graph plots the Column i and Column j number as well as the mutual information shared between them. This is done by MATLAB surface fitting tool. As you can see, the spikes are where the mutual information is highest between the two columns. The peaks are where pairing is most likely to occur because they share the most information in most of the sequences. .
This 2D plot plots Column number versus the entropy of that column. Entropy is lowest when the that area of the sequence is the most conserved. As one can see, the most conserved area is probably position 61-71. Important structures of the tRNA may be encoded there.
| I | Attachment | Action | Size | Date | Who | Comment |
|---|---|---|---|---|---|---|
 png |
Entropy.png | manage | 74.7 K | 2011-11-20 - 23:09 | TaiNg | |
| png |
Mutual.png | manage | 120.8 K | 2011-11-20 - 22:18 | TaiNg | |
 txt |
info.pl.txt | manage | 7.6 K | 2011-11-22 - 05:27 | TaiNg | Without comment |
| txt |
info2.pl.txt | manage | 7.6 K | 2011-11-22 - 05:29 | TaiNg | With comment |
 EXT |
mastertest | manage | 158.9 K | 2011-11-22 - 05:32 | TaiNg | tRNA test file |
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